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Kuszczynska A, Bors M, Podskoczyj K, Leszczynska G. Chemistry of installing epitranscriptomic 5-modified cytidines in RNA oligomers. Org Biomol Chem 2024. [PMID: 39177469 DOI: 10.1039/d4ob01098a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
Studies of 5-hydroxymethylcytidine (hm5C), 5-formylcytidine (f5C) and 5-carboxycytidine (ca5C) modifications as products of the 5-methylcytidine (m5C) oxidative demethylation pathway in cellular mRNAs constitute an important element of the new epitranscriptomic field of research. The dynamic process of m5C conversion and final turnover to the parent cytidine is considered a post-transcriptional layer of gene-expression regulation. However, the regulatory mechanism associated with epitranscriptomic cytidine modifications remains largely unknown. Therefore, oligonucleotides containing m5C oxidation products are of great value for the next generation of biochemical, biophysical, and structural studies on their function, metabolism, and contribution to human diseases. Herein, we summarize the synthetic strategies developed for the incorporation of hm5C, f5C and ca5C into RNA oligomers by phosphoramidite chemistry, including post-synthetic C5-cytidine functionalization and enzymatic methods.
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Affiliation(s)
- Anna Kuszczynska
- Institute of Organic Chemistry, Faculty of Chemistry, University of Technology, 90-924 Lodz, Zeromskiego 116, Poland.
| | - Milena Bors
- Institute of Organic Chemistry, Faculty of Chemistry, University of Technology, 90-924 Lodz, Zeromskiego 116, Poland.
| | - Karolina Podskoczyj
- Institute of Organic Chemistry, Faculty of Chemistry, University of Technology, 90-924 Lodz, Zeromskiego 116, Poland.
| | - Grazyna Leszczynska
- Institute of Organic Chemistry, Faculty of Chemistry, University of Technology, 90-924 Lodz, Zeromskiego 116, Poland.
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2
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Zhang L, Huang X, Wang D, Fan C, Jiang H, Xie D. Transcriptomic evaluation of N6-methyladenosine modification can be used to identify differentially gene and immune-related biological processes in TX mice with liver fibrosis. Mol Biol Rep 2024; 51:149. [PMID: 38236359 DOI: 10.1007/s11033-023-09163-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/14/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND N6-methyladenosine (m6A) modification controls the stability, splicing, and translation of mRNA, which is important in the development of illnesses. Wilson's disease (WD) is an autosomal recessive liver copper metabolic disorder that causes liver fibrosis. The role of m6A methylation in WD-induced liver fibrosis development is still unclear. Thus, the goal of this study was to examine the scope of m6A methylation and further explore the potential targets related to WD-induced liver fibrosis. RESULTS A total of 1930 significantly different m6A peaks were found on 1737 mRNAs, of which 993 were hypermethylated and 744 were hypomethylated when comparing normal and WD-induced liver fibrosis mice (n = 3). In parallel, 1261 differentially expressed mRNAs, comprising 557 upregulated and 704 downregulated mRNAs, were found. Overall, 114 mRNAs with significant changes in m6A levels and RNA expression were identified via joint analysis. Then, through PPI network construction and functional enrichment analysis, 12 hub genes were identified, these genes were mainly enriched in the inflammatory response and immunomodulation, and they are associated with immune cell infiltration. CONCLUSIONS The significant difference in the amount of mRNA m6A modifications indicates that m6A modification is involved in the progression of WD-induced liver fibrosis, and theidentified hub genes are involved in inflammation and immune infiltration. These results may provide insights for subsequent studies on potential regulatory mechanisms.
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Affiliation(s)
- Lili Zhang
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Xiaofeng Huang
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Dan Wang
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Chang Fan
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Hui Jiang
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China.
| | - Daojun Xie
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.
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3
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Pierattini B, D’Agostino S, Bon C, Peruzzo O, Alendar A, Codino A, Ros G, Persichetti F, Sanges R, Carninci P, Santoro C, Espinoza S, Valentini P, Pandolfini L, Gustincich S. SINEUP non-coding RNA activity depends on specific N6-methyladenosine nucleotides. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:402-414. [PMID: 37187707 PMCID: PMC10176434 DOI: 10.1016/j.omtn.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023]
Abstract
SINEUPs are natural and synthetic antisense long non-coding RNAs (lncRNAs) selectively enhancing target mRNAs translation by increasing their association with polysomes. This activity requires two RNA domains: an embedded inverted SINEB2 element acting as effector domain, and an antisense region, the binding domain, conferring target selectivity. SINEUP technology presents several advantages to treat genetic (haploinsufficiencies) and complex diseases restoring the physiological activity of diseased genes and of compensatory pathways. To streamline these applications to the clinic, a better understanding of the mechanism of action is needed. Here we show that natural mouse SINEUP AS Uchl1 and synthetic human miniSINEUP-DJ-1 are N6-methyladenosine (m6A) modified by METTL3 enzyme. Then, we map m6A-modified sites along SINEUP sequence with Nanopore direct RNA sequencing and a reverse transcription assay. We report that m6A removal from SINEUP RNA causes the depletion of endogenous target mRNA from actively translating polysomes, without altering SINEUP enrichment in ribosomal subunit-associated fractions. These results prove that SINEUP activity requires an m6A-dependent step to enhance translation of target mRNAs, providing a new mechanism for m6A translation regulation and strengthening our knowledge of SINEUP-specific mode of action. Altogether these new findings pave the way to a more effective therapeutic application of this well-defined class of lncRNAs.
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Affiliation(s)
- Bianca Pierattini
- Area of Neuroscience, International School for Advanced Studies (SISSA), Trieste, Italy
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Sabrina D’Agostino
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Carlotta Bon
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Omar Peruzzo
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Andrej Alendar
- The Gurdon Institute and Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Azzurra Codino
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Gloria Ros
- Department of Health Sciences and Research Center on Autoimmune and Allergic Diseases (CAAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Francesca Persichetti
- Department of Health Sciences and Research Center on Autoimmune and Allergic Diseases (CAAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Remo Sanges
- Area of Neuroscience, International School for Advanced Studies (SISSA), Trieste, Italy
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences (IMS), Yokohama 230-0045, Japan
- Human Technopole, 20157 Milan, Italy
| | - Claudio Santoro
- Department of Health Sciences and Research Center on Autoimmune and Allergic Diseases (CAAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Stefano Espinoza
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
- Department of Health Sciences and Research Center on Autoimmune and Allergic Diseases (CAAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Paola Valentini
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
- Corresponding author: Paola Valentini, Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), via Melen 83, 16152 Genova, Italy.
| | - Luca Pandolfini
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
- Corresponding author: Luca Pandolfini, Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), via Melen 83, 16152 Genova, Italy.
| | - Stefano Gustincich
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
- Corresponding author: Stefano Gustincich, Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), via Melen 83, 16152 Genova, Italy.
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4
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Enguita FJ, Leitão AL, Mattick JS. RNA Regulatory Networks 2.0. Int J Mol Sci 2023; 24:ijms24109001. [PMID: 37240347 DOI: 10.3390/ijms24109001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
The central role of RNA molecules in cell biology has been an expanding subject of study since the proposal of the "RNA world" hypothesis 60 years ago [...].
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Affiliation(s)
- Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Ana Lúcia Leitão
- Department of Chemistry, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
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5
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Podskoczyj K, Klos A, Drewniak S, Leszczynska G. Two-step conversion of uridine and cytidine to variously C5-C functionalized analogs. Org Biomol Chem 2023; 21:2809-2815. [PMID: 36924236 DOI: 10.1039/d3ob00161j] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
C5-substituted pyrimidine nucleosides are an important class of molecules that have practical use as biological probes and pharmaceuticals. Herein we report an operationally simple protocol for C5-functionalization of uridine and cytidine via transformation of underexploited 5-trifluoromethyluridine or 5-trifluoromethylcytidine, respectively. The unique reactivity of the CF3 group in the aromatic ring allowed the direct incorporation of several distinct C5-C "carbon substituents": carboxyl, nitrile, ester, amide, and amidine.
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Affiliation(s)
- Karolina Podskoczyj
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Lodz 90-924, Poland.
| | - Anna Klos
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Lodz 90-924, Poland.
| | - Szymon Drewniak
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Lodz 90-924, Poland.
| | - Grazyna Leszczynska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Lodz 90-924, Poland.
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6
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Qin H, Sheng W, Weng J, Li G, Chen Y, Zhu Y, Wang Q, Chen Y, Yang Q, Yu F, Zeng H, Xiong A. Identification and verification of m7G-Related genes as biomarkers for prognosis of sarcoma. Front Genet 2023; 14:1101683. [PMID: 36816047 PMCID: PMC9935680 DOI: 10.3389/fgene.2023.1101683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
Background: Increasing evidence indicates a crucial role for N7-methylguanosine (m7G) methylation modification in human disease development, particularly cancer, and aberrant m7G levels are closely associated with tumorigenesis and progression via regulation of the expression of multiple oncogenes and tumor suppressor genes. However, the role of m7G in sarcomas (SARC) has not been adequately evaluated. Materials and methods: Transcriptome and clinical data were gathered from the TCGA database for this study. Normal and SARC groups were compared for the expression of m7G-related genes (m7GRGs). The expression of m7GRGs was verified using real-time quantitative PCR (RT-qPCR) in SARC cell lines. Then, differentially expressed genes (DEGs) were identified between high and low m7GRGs expression groups in SARC samples, and GO enrichment and KEGG pathways were evaluated. Next, prognostic values of m7GRGs were evaluated by Cox regression analysis. Subsequently, a prognostic model was constructed using m7GRGs with good prognostic values by Lasso regression analysis. Besides, the relationships between prognostic m7GRGs and immune infiltration, clinical features, cuproptosis-related genes, and antitumor drugs were investigated in patients with SARC. Finally, a ceRNA regulatory network based on m7GRGs was constructed. Results: The expression of ten m7GRGs was higher in the SARC group than in the control group. DEGs across groups with high and low m7GRGs expression were enriched for adhesion sites and cGMP-PKG. Besides, we constructed a prognostic model that consists of EIF4A1, EIF4G3, NCBP1, and WDR4 m7GRGs for predicting the survival likelihood of sarcoma patients. And the elevated expression of these four prognostic m7GRGs was substantially associated with poor prognosis and elevated expression in SARC cell lines. Moreover, we discovered that these four m7GRGs expressions were negatively correlated with CD4+ T cell levels, dendritic cell level and tumor purity, and positively correlated with tumor mutational burden, microsatellite instability, drug sensitivity and cuproptosis-related genes in patients with sarcomas. Then, a triple regulatory network of mRNA, miRNA, and lncRNA was established. Conclusion: The current study identified EIF4A1, EIF4G3, NCBP1, and WDR4 as prognostic genes for SARC that are associated with m7G.These findings extend our knowledge of m7G methylation in SARC and may guide the development of innovative treatment options.
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Affiliation(s)
- Haotian Qin
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen, China,Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Weibei Sheng
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen, China,Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Jian Weng
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen, China,Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Guoqing Li
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen, China,Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yingqi Chen
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen, China,Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yuanchao Zhu
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen, China,Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Qichang Wang
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen, China,Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yixiao Chen
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen, China,Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Qi Yang
- Department of Medical Ultrasound, Peking University Shenzhen Hospital, Shenzhen, China
| | - Fei Yu
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen, China,Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China,*Correspondence: Fei Yu, ; Hui Zeng, ; Ao Xiong,
| | - Hui Zeng
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen, China,Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China,*Correspondence: Fei Yu, ; Hui Zeng, ; Ao Xiong,
| | - Ao Xiong
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen, China,Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China,*Correspondence: Fei Yu, ; Hui Zeng, ; Ao Xiong,
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7
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Petri BJ, Klinge CM. m6A readers, writers, erasers, and the m6A epitranscriptome in breast cancer. J Mol Endocrinol 2023; 70:JME-22-0110. [PMID: 36367225 PMCID: PMC9790079 DOI: 10.1530/jme-22-0110] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/11/2022] [Indexed: 11/13/2022]
Abstract
Epitranscriptomic modification of RNA regulates human development, health, and disease. The true diversity of the transcriptome in breast cancer including chemical modification of transcribed RNA (epitranscriptomics) is not well understood due to limitations of technology and bioinformatic analysis. N-6-methyladenosine (m6A) is the most abundant epitranscriptomic modification of mRNA and regulates splicing, stability, translation, and intracellular localization of transcripts depending on m6A association with reader RNA-binding proteins. m6A methylation is catalyzed by the METTL3 complex and removed by specific m6A demethylase ALKBH5, with the role of FTO as an 'eraser' uncertain. In this review, we provide an overview of epitranscriptomics related to mRNA and focus on m6A in mRNA and its detection. We summarize current knowledge on altered levels of writers, readers, and erasers of m6A and their roles in breast cancer and their association with prognosis. We summarize studies identifying m6A peaks and sites in genes in breast cancer cells.
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Affiliation(s)
- Belinda J. Petri
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292 USA
| | - Carolyn M. Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292 USA
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS)
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8
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Zha L, Wang J, Cheng X. The effects of
RNA
methylation on immune cells development and function. FASEB J 2022; 36:e22552. [DOI: 10.1096/fj.202200716r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/23/2022] [Accepted: 09/06/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Ling‐Feng Zha
- Department of Cardiology Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Biological Targeted Therapy, Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases Wuhan China
| | - Jing‐Lin Wang
- Department of Cardiology Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Biological Targeted Therapy, Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases Wuhan China
| | - Xiang Cheng
- Department of Cardiology Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Key Laboratory of Biological Targeted Therapy, Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases Wuhan China
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9
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Integrated Analysis and Identification of Critical RNA-Binding Proteins in Bladder Cancer. Cancers (Basel) 2022; 14:cancers14153739. [PMID: 35954405 PMCID: PMC9367304 DOI: 10.3390/cancers14153739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/20/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The role of RNA-binding proteins (RBPs) in bladder cancer (BC) remains unclear. Therefore, we analyzed the clinical information and RNA sequencing data from patients with BC and identified RBPs that may be promising predictors of BC. Abstract RBPs in the development and progression of BC remains unclear. Here, we elucidated the role of RBPs in predicting the survival of patients with BC. Clinical information and RNA sequencing data of the training and validation cohorts were downloaded from the Cancer Genome Atlas and Gene Expression Omnibus databases, respectively. Survival-related differentially expressed RBPs were identified using Cox regression analyses. A total of 113 upregulated and 54 downregulated RBPs were observed, with six showing prognostic values (AHNAK, MAP1B, LAMA2, P4HB, FASN, and GSDMB). In both the GSE32548 and GSE31684 datasets, patients with low-risk scores in survival-related six RBPs-based prognostic model showed longer overall survival than those with high-risk scores. AHNAK, MAP1B, P4HB, and FASN expression were significantly upregulated in both BC tissues and cell lines. BC tissues from high-risk group showed higher proportions of naive CD4+ T cells, M0 and M2 macrophages, and neutrophils and lower proportions of plasma cells, CD8+ T cells, and T-cell follicular helper compared to low-risk group. AHNAK knockdown significantly inhibited the proliferation, invasion, and migration of BC cells in vitro and inhibited the growth of subcutaneous tumors in vivo. We thus developed and functionally validated a novel six RBPs-based prognostic model for BC.
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Regulation of N6-Methyladenosine after Myocardial Infarction. Cells 2022; 11:cells11152271. [PMID: 35892568 PMCID: PMC9329994 DOI: 10.3390/cells11152271] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 12/10/2022] Open
Abstract
Development of heart failure (HF) after myocardial infarction (MI) is responsible for premature death. Complex cellular and molecular mechanisms are involved in this process. A number of studies have linked the epitranscriptomic RNA modification N6-methyladenosine (m6A) with HF, but it remains unknown how m6A affects the risk of developing HF after MI. We addressed the regulation of m6A and its demethylase fat mass and obesity-associated (FTO) after MI and their association with HF. Using liquid chromatography coupled to mass spectrometry, we observed an increase of m6A content in the infarcted area of rat hearts subjected to coronary ligation and a decrease in blood. FTO expression measured by quantitative PCR was downregulated in the infarcted hearts. In whole blood samples collected at the time of reperfusion in MI patients, m6A content was lower in patients who developed HF as attested by a 4-month ejection fraction (EF) of ≤40% as compared to patients who did not develop HF (EF > 50%). M6A content was higher in females. These results show that m6A measured in blood is associated with HF development after MI and motivate further investigation of the potential role of m6A as a novel epitranscriptomics biomarker and therapeutic target of HF.
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11
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Wu JY, Song QY, Huang CZ, Shao Y, Wang ZL, Zhang HQ, Fu Z. N7-methylguanosine-related lncRNAs: Predicting the prognosis and diagnosis of colorectal cancer in the cold and hot tumors. Front Genet 2022; 13:952836. [PMID: 35937987 PMCID: PMC9352958 DOI: 10.3389/fgene.2022.952836] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Background: 7-Methylguanosine(m7G) contributes greatly to its pathogenesis and progression in colorectal cancer. We proposed building a prognostic model of m7G-related LncRNAs. Our prognostic model was used to identify differences between hot and cold tumors.Methods: The study included 647 colorectal cancer patients (51 cancer-free patients and 647 cancer patients) from The Cancer Genome Atlas (TCGA). We identified m7G-related prognostic lncRNAs by employing the univariate Cox regression method. Assessments were conducted using univariate Cox regression, multivariate Cox regression, receiver operating characteristics (ROC), nomogram, calibration curves, and Kaplan-Meier analysis. All of these procedures were used with the aim of confirming the validity and stability of the model. Besides these two analyses, we also conducted half-maximal inhibitory concentration (IC50), immune analysis, principal component analysis (PCA), and gene set enrichment analysis (GSEA). The entire set of m7G-related (lncRNAs) with respect to cold and hot tumors has been divided into two clusters for further discussion of immunotherapy.Results: The risk model was constructed with 17 m7G-related lncRNAs. A good correlation was found between the calibration plots and the prognosis prediction in the model. By assessing IC50 in a significant way across risk groups, systemic treatment can be guided. By using clusters, it may be possible to distinguish hot and cold tumors effectively and to aid in specific therapeutic interventions. Cluster 1 was identified as having the highest response to immunotherapy drugs and thus was identified as the hot tumor.Conclusion: This study shows that 17 m7G-related lncRNA can be used in clinical settings to predict prognosis and use them to determine whether a tumor is cold or hot in colorectal cancer and improve the individualization of treatment.
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Affiliation(s)
- Jing-Yu Wu
- The General Surgery Laboratory, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qing-Yu Song
- The General Surgery Laboratory, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chang-Zhi Huang
- The General Surgery Laboratory, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yu Shao
- The General Surgery Laboratory, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhen-Ling Wang
- The General Surgery Laboratory, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hong-Qiang Zhang
- The General Surgery Laboratory, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zan Fu
- The General Surgery Laboratory, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Zan Fu,
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12
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Aslam M, Huang X, Yan M, She Z, Lu X, Fakher B, Chen Y, Li G, Qin Y. TRM61 is essential for Arabidopsis embryo and endosperm development. PLANT REPRODUCTION 2022; 35:31-46. [PMID: 34406456 DOI: 10.1007/s00497-021-00428-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
Post-transcriptional modifications of tRNA molecules play crucial roles in gene expression and protein biosynthesis. Across the genera, methylation of tRNAs at N1 of adenosine 58 (A58) by AtTRM61/AtTRM6 complex plays a critical role in maintaining the stability of initiator methionyl-tRNA (tRNAiMet). Recently, it was shown that mutation in AtTRM61 or AtTRM6 leads to seed abortion. However, a detailed study about the AtTRM61/AtTRM6 function in plants remains vague. Here, we found that AtTRM61 has a conserved functional structure and possesses conserved binding motifs for cofactor S-adenosyl-L-methionine (AdoMet). Mutations of the complex subunits AtTRM61/AtTRM6 result in embryo and endosperm developmental defects. The endosperm and embryo developmental defects were conditionally complemented by Attrm61-1/ + FIS2pro::AtTRM61 and Attrm61-1/ + ABI3pro::AtTRM61 indicating that AtTRM61 is required for early embryo and endosperm development. Besides, the rescue of the fertility defects in trm61/ + by overexpression of initiator tRNA suggests that AtTRM61 mutation could diminish tRNAiMet stability. Moreover, using yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays, we showed that AtMPK4 physically interacts with AtTRM61. The data presented here suggest that AtTRM61 has a conserved structure and function in Arabidopsis. Also, AtTRM61 may be required for tRNAiMet stability, embryo and endosperm development.
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Affiliation(s)
- Mohammad Aslam
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Xiaoyi Huang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Maokai Yan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Zeyuan She
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Xiangyu Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Beenish Fakher
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yingzhi Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Gang Li
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Yuan Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China.
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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13
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Qi TF, Miao W, Wang Y. Targeted Profiling of Epitranscriptomic Reader, Writer, and Eraser Proteins Accompanied with Radioresistance in Breast Cancer Cells. Anal Chem 2022; 94:1525-1530. [PMID: 35021009 PMCID: PMC8792366 DOI: 10.1021/acs.analchem.1c05441] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Epitranscriptomic reader, writer, and eraser (RWE) proteins recognize, install, and remove modified nucleosides in RNA, which are known to play crucial roles in RNA processing, splicing, and stability. Here, we established a liquid chromatography-parallel-reaction monitoring (LC-PRM) method for high-throughput profiling of a total of 152 epitranscriptomic RWE proteins. We also applied the LC-PRM method, in conjunction with stable isotope labeling by amino acids in cell culture (SILAC), to quantify these proteins in two pairs of matched parental/radioresistant breast cancer cells (i.e., MDA-MB-231 and MCF-7 cells and their corresponding radioresistant C5 and C6 clones), with the goal of assessing the roles of these proteins in radioresistance. We found that eight epitranscriptomic RWE proteins were commonly altered by over 1.5-fold in the two pairs of breast cancer cells. Among them, TRMT1 (an m2,2G writer) may play a role in promoting breast cancer radioresistance due to its clinical relevance and its correlation with DNA repair gene sets. To our knowledge, this is the first report of a targeted proteomic method for comprehensive quantifications of epitranscriptomic RWE proteins. We envision that the LC-PRM method is applicable for studying the roles of these proteins in the metastatic transformation of cancer and therapeutic resistance of other types of cancer in the future.
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14
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Morozova A, Zorkina Y, Abramova O, Pavlova O, Pavlov K, Soloveva K, Volkova M, Alekseeva P, Andryshchenko A, Kostyuk G, Gurina O, Chekhonin V. Neurobiological Highlights of Cognitive Impairment in Psychiatric Disorders. Int J Mol Sci 2022; 23:1217. [PMID: 35163141 PMCID: PMC8835608 DOI: 10.3390/ijms23031217] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 02/07/2023] Open
Abstract
This review is focused on several psychiatric disorders in which cognitive impairment is a major component of the disease, influencing life quality. There are plenty of data proving that cognitive impairment accompanies and even underlies some psychiatric disorders. In addition, sources provide information on the biological background of cognitive problems associated with mental illness. This scientific review aims to summarize the current knowledge about neurobiological mechanisms of cognitive impairment in people with schizophrenia, depression, mild cognitive impairment and dementia (including Alzheimer's disease).The review provides data about the prevalence of cognitive impairment in people with mental illness and associated biological markers.
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Affiliation(s)
- Anna Morozova
- Mental-Health Clinic No. 1 Named after N.A. Alekseev, 117152 Moscow, Russia; (A.M.); (O.A.); (K.S.); (M.V.); (P.A.); (A.A.); (G.K.)
- Department of Basic and Applied Neurobiology, V. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia; (O.P.); (K.P.); (O.G.); (V.C.)
| | - Yana Zorkina
- Mental-Health Clinic No. 1 Named after N.A. Alekseev, 117152 Moscow, Russia; (A.M.); (O.A.); (K.S.); (M.V.); (P.A.); (A.A.); (G.K.)
- Department of Basic and Applied Neurobiology, V. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia; (O.P.); (K.P.); (O.G.); (V.C.)
| | - Olga Abramova
- Mental-Health Clinic No. 1 Named after N.A. Alekseev, 117152 Moscow, Russia; (A.M.); (O.A.); (K.S.); (M.V.); (P.A.); (A.A.); (G.K.)
- Department of Basic and Applied Neurobiology, V. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia; (O.P.); (K.P.); (O.G.); (V.C.)
| | - Olga Pavlova
- Department of Basic and Applied Neurobiology, V. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia; (O.P.); (K.P.); (O.G.); (V.C.)
| | - Konstantin Pavlov
- Department of Basic and Applied Neurobiology, V. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia; (O.P.); (K.P.); (O.G.); (V.C.)
| | - Kristina Soloveva
- Mental-Health Clinic No. 1 Named after N.A. Alekseev, 117152 Moscow, Russia; (A.M.); (O.A.); (K.S.); (M.V.); (P.A.); (A.A.); (G.K.)
| | - Maria Volkova
- Mental-Health Clinic No. 1 Named after N.A. Alekseev, 117152 Moscow, Russia; (A.M.); (O.A.); (K.S.); (M.V.); (P.A.); (A.A.); (G.K.)
| | - Polina Alekseeva
- Mental-Health Clinic No. 1 Named after N.A. Alekseev, 117152 Moscow, Russia; (A.M.); (O.A.); (K.S.); (M.V.); (P.A.); (A.A.); (G.K.)
| | - Alisa Andryshchenko
- Mental-Health Clinic No. 1 Named after N.A. Alekseev, 117152 Moscow, Russia; (A.M.); (O.A.); (K.S.); (M.V.); (P.A.); (A.A.); (G.K.)
| | - Georgiy Kostyuk
- Mental-Health Clinic No. 1 Named after N.A. Alekseev, 117152 Moscow, Russia; (A.M.); (O.A.); (K.S.); (M.V.); (P.A.); (A.A.); (G.K.)
| | - Olga Gurina
- Department of Basic and Applied Neurobiology, V. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia; (O.P.); (K.P.); (O.G.); (V.C.)
| | - Vladimir Chekhonin
- Department of Basic and Applied Neurobiology, V. Serbsky Federal Medical Research Centre of Psychiatry and Narcology, 119034 Moscow, Russia; (O.P.); (K.P.); (O.G.); (V.C.)
- Department of Medical Nanobiotechnology, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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15
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Larizza L, Calzari L, Alari V, Russo S. Genes for RNA-binding proteins involved in neural-specific functions and diseases are downregulated in Rubinstein-Taybi iNeurons. Neural Regen Res 2022; 17:5-14. [PMID: 34100419 PMCID: PMC8451555 DOI: 10.4103/1673-5374.314286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Taking advantage of the fast-growing knowledge of RNA-binding proteins (RBPs) we review the signature of downregulated genes for RBPs in the transcriptome of induced pluripotent stem cell neurons (iNeurons) modelling the neurodevelopmental Rubinstein Taybi Syndrome (RSTS) caused by mutations in the genes encoding CBP/p300 acetyltransferases. We discuss top and functionally connected downregulated genes sorted to “RNA processing” and “Ribonucleoprotein complex biogenesis” Gene Ontology clusters. The first set of downregulated RBPs includes members of hnRNHP (A1, A2B1, D, G, H2-H1, MAGOHB, PAPBC), core subunits of U small nuclear ribonucleoproteins and Serine-Arginine splicing regulators families, acting in precursor messenger RNA alternative splicing and processing. Consistent with literature findings on reduced transcript levels of serine/arginine repetitive matrix 4 (SRRM4) protein, the main regulator of the neural-specific microexons splicing program upon depletion of Ep300 and Crebbp in mouse neurons, RSTS iNeurons show downregulated genes for proteins impacting this network. We link downregulated genes to neurological disorders including the new HNRNPH1-related intellectual disability syndrome with clinical overlap to RSTS. The set of downregulated genes for Ribosome biogenesis includes several components of ribosomal subunits and nucleolar proteins, such NOP58 and fibrillarin that form complexes with snoRNAs with a central role in guiding post-transcriptional modifications needed for rRNA maturation. These nucleolar proteins are “dual” players as fibrillarin is also required for epigenetic regulation of ribosomal genes and conversely NOP58-associated snoRNA levels are under the control of NOP58 interactor BMAL1, a transcriptional regulator of the circadian rhythm. Additional downregulated genes for “dual specificity” RBPs such as RUVBL1 and METTL1 highlight the links between chromatin and the RBP-ome and the contribution of perturbations in their cross-talk to RSTS. We underline the hub position of CBP/p300 in chromatin regulation, the impact of its defect on neurons’ post-transcriptional regulation of gene expression and the potential use of epidrugs in therapeutics of RBP-caused neurodevelopmental disorders.
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Affiliation(s)
- Lidia Larizza
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Luciano Calzari
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Valentina Alari
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Silvia Russo
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
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16
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Leger A, Amaral PP, Pandolfini L, Capitanchik C, Capraro F, Miano V, Migliori V, Toolan-Kerr P, Sideri T, Enright AJ, Tzelepis K, van Werven FJ, Luscombe NM, Barbieri I, Ule J, Fitzgerald T, Birney E, Leonardi T, Kouzarides T. RNA modifications detection by comparative Nanopore direct RNA sequencing. Nat Commun 2021; 12:7198. [PMID: 34893601 PMCID: PMC8664944 DOI: 10.1038/s41467-021-27393-3] [Citation(s) in RCA: 149] [Impact Index Per Article: 49.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/09/2021] [Indexed: 12/23/2022] Open
Abstract
RNA molecules undergo a vast array of chemical post-transcriptional modifications (PTMs) that can affect their structure and interaction properties. In recent years, a growing number of PTMs have been successfully mapped to the transcriptome using experimental approaches relying on high-throughput sequencing. Oxford Nanopore direct-RNA sequencing has been shown to be sensitive to RNA modifications. We developed and validated Nanocompore, a robust analytical framework that identifies modifications from these data. Our strategy compares an RNA sample of interest against a non-modified control sample, not requiring a training set and allowing the use of replicates. We show that Nanocompore can detect different RNA modifications with position accuracy in vitro, and we apply it to profile m6A in vivo in yeast and human RNAs, as well as in targeted non-coding RNAs. We confirm our results with orthogonal methods and provide novel insights on the co-occurrence of multiple modified residues on individual RNA molecules.
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Affiliation(s)
- Adrien Leger
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Oxford Nanopore Technologies, Gosling Building, Oxford Science Park, Oxford, UK
| | - Paulo P Amaral
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, UK
- The Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, UK
- INSPER - Institute of Education and Research, São Paulo, SP, Brazil
| | - Luca Pandolfini
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, UK
- Istituto Italiano di Tecnologia (IIT), Center for Human Technologies (CHT), Genova, Italy
| | | | - Federica Capraro
- The Francis Crick Institute, London, UK
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | - Valentina Miano
- Department of Pathology, Division of Cellular and Molecular Pathology, University of Cambridge, Cambridge, UK
| | - Valentina Migliori
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Patrick Toolan-Kerr
- The Francis Crick Institute, London, UK
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | | | - Anton J Enright
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK
| | | | | | - Nicholas M Luscombe
- The Francis Crick Institute, London, UK
- Department of Genetics, Environment and Evolution, UCL Genetics Institute, London, UK
- Okinawa Institute of Science & Technology Graduate University, Okinawa, Japan
| | - Isaia Barbieri
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, UK
- Department of Pathology, Division of Cellular and Molecular Pathology, University of Cambridge, Cambridge, UK
| | - Jernej Ule
- The Francis Crick Institute, London, UK
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | - Tomas Fitzgerald
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Tommaso Leonardi
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, UK.
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy.
| | - Tony Kouzarides
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, UK.
- The Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, UK.
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17
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RNA Modifications and RNA Metabolism in Neurological Disease Pathogenesis. Int J Mol Sci 2021; 22:ijms222111870. [PMID: 34769301 PMCID: PMC8584444 DOI: 10.3390/ijms222111870] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/16/2021] [Accepted: 10/26/2021] [Indexed: 02/06/2023] Open
Abstract
The intrinsic cellular heterogeneity and molecular complexity of the mammalian nervous system relies substantially on the dynamic nature and spatiotemporal patterning of gene expression. These features of gene expression are achieved in part through mechanisms involving various epigenetic processes such as DNA methylation, post-translational histone modifications, and non-coding RNA activity, amongst others. In concert, another regulatory layer by which RNA bases and sugar residues are chemically modified enhances neuronal transcriptome complexity. Similar RNA modifications in other systems collectively constitute the cellular epitranscriptome that integrates and impacts various physiological processes. The epitranscriptome is dynamic and is reshaped constantly to regulate vital processes such as development, differentiation and stress responses. Perturbations of the epitranscriptome can lead to various pathogenic conditions, including cancer, cardiovascular abnormalities and neurological diseases. Recent advances in next-generation sequencing technologies have enabled us to identify and locate modified bases/sugars on different RNA species. These RNA modifications modulate the stability, transport and, most importantly, translation of RNA. In this review, we discuss the formation and functions of some frequently observed RNA modifications—including methylations of adenine and cytosine bases, and isomerization of uridine to pseudouridine—at various layers of RNA metabolism, together with their contributions to abnormal physiological conditions that can lead to various neurodevelopmental and neurological disorders.
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18
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Caudai C, Galizia A, Geraci F, Le Pera L, Morea V, Salerno E, Via A, Colombo T. AI applications in functional genomics. Comput Struct Biotechnol J 2021; 19:5762-5790. [PMID: 34765093 PMCID: PMC8566780 DOI: 10.1016/j.csbj.2021.10.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 10/05/2021] [Accepted: 10/05/2021] [Indexed: 12/13/2022] Open
Abstract
We review the current applications of artificial intelligence (AI) in functional genomics. The recent explosion of AI follows the remarkable achievements made possible by "deep learning", along with a burst of "big data" that can meet its hunger. Biology is about to overthrow astronomy as the paradigmatic representative of big data producer. This has been made possible by huge advancements in the field of high throughput technologies, applied to determine how the individual components of a biological system work together to accomplish different processes. The disciplines contributing to this bulk of data are collectively known as functional genomics. They consist in studies of: i) the information contained in the DNA (genomics); ii) the modifications that DNA can reversibly undergo (epigenomics); iii) the RNA transcripts originated by a genome (transcriptomics); iv) the ensemble of chemical modifications decorating different types of RNA transcripts (epitranscriptomics); v) the products of protein-coding transcripts (proteomics); and vi) the small molecules produced from cell metabolism (metabolomics) present in an organism or system at a given time, in physiological or pathological conditions. After reviewing main applications of AI in functional genomics, we discuss important accompanying issues, including ethical, legal and economic issues and the importance of explainability.
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Affiliation(s)
- Claudia Caudai
- CNR, Institute of Information Science and Technologies “A. Faedo” (ISTI), Pisa, Italy
| | - Antonella Galizia
- CNR, Institute of Applied Mathematics and Information Technologies (IMATI), Genoa, Italy
| | - Filippo Geraci
- CNR, Institute for Informatics and Telematics (IIT), Pisa, Italy
| | - Loredana Le Pera
- CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy
- CNR, Institute of Molecular Biology and Pathology (IBPM), Rome, Italy
| | - Veronica Morea
- CNR, Institute of Molecular Biology and Pathology (IBPM), Rome, Italy
| | - Emanuele Salerno
- CNR, Institute of Information Science and Technologies “A. Faedo” (ISTI), Pisa, Italy
| | - Allegra Via
- CNR, Institute of Molecular Biology and Pathology (IBPM), Rome, Italy
| | - Teresa Colombo
- CNR, Institute of Molecular Biology and Pathology (IBPM), Rome, Italy
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19
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Klinge CM, Piell KM, Petri BJ, He L, Zhang X, Pan J, Rai SN, Andreeva K, Rouchka EC, Wahlang B, Beier JI, Cave MC. Combined exposure to polychlorinated biphenyls and high-fat diet modifies the global epitranscriptomic landscape in mouse liver. ENVIRONMENTAL EPIGENETICS 2021; 7:dvab008. [PMID: 34548932 PMCID: PMC8448424 DOI: 10.1093/eep/dvab008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/13/2021] [Accepted: 08/10/2021] [Indexed: 05/30/2023]
Abstract
Exposure to a single dose of polychlorinated biphenyls (PCBs) and a 12-week high-fat diet (HFD) results in nonalcoholic steatohepatitis (NASH) in mice by altering intracellular signaling and inhibiting epidermal growth factor receptor signaling. Post-transcriptional chemical modification (PTM) of RNA regulates biological processes, but the contribution of epitranscriptomics to PCB-induced steatosis remains unknown. This study tested the hypothesis that PCB and HFD exposure alters the global RNA epitranscriptome in male mouse liver. C57BL/6J male mice were fed a HFD for 12 weeks and exposed to a single dose of Aroclor 1260 (20 mg/kg), PCB 126 (20 µg/kg), both Aroclor 1260 and PCB 126 or vehicle control after 2 weeks on HFD. Chemical RNA modifications were identified at the nucleoside level by liquid chromatography-mass spectrometry. From 22 PTM global RNA modifications, we identified 10 significant changes in RNA modifications in liver with HFD and PCB 126 exposure. Only two modifications were significantly different from HFD control liver in all three PCB exposure groups: 2'-O-methyladenosine (Am) and N(6)-methyladenosine (m6A). Exposure to HFD + PCB 126 + Aroclor 1260 increased the abundance of N(6), O(2)-dimethyladenosine (m6Am), which is associated with the largest number of transcript changes. Increased m6Am and pseudouridine were associated with increased protein expression of the writers of these modifications: Phosphorylated CTD Interacting Factor 1 (PCIF1) and Pseudouridine Synthase 10 (PUS10), respectively, in HFD + PCB 126- + Aroclor 1260-exposed mouse liver. Increased N1-methyladenosine (m1A) and m6A were associated with increased transcript levels of the readers of these modifications: YTH N6-Methyladenosine RNA Binding Protein 2 (YTHDF2), YTH Domain Containing 2 (YTHDC2), and reader FMRP Translational Regulator 1 (FMR1) transcript and protein abundance. The results demonstrate that PCB exposure alters the global epitranscriptome in a mouse model of NASH; however, the mechanism for these changes requires further investigation.
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Affiliation(s)
- Carolyn M Klinge
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
| | - Kellianne M Piell
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Belinda J Petri
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Liqing He
- Department of Chemistry, University of Louisville College of Arts and Sciences, Louisville, KY 40292, USA
| | - Xiang Zhang
- Department of Chemistry, University of Louisville College of Arts and Sciences, Louisville, KY 40292, USA
- University of Louisville Hepatobiology and Toxicology Center, Louisville, KY 40292, USA
- University of Louisville Alcohol Research Center, Louisville, KY 40292, USA
| | - Jianmin Pan
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
- Biostatistics and Bioinformatics Facility, James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Shesh N Rai
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
- University of Louisville Hepatobiology and Toxicology Center, Louisville, KY 40292, USA
- University of Louisville Alcohol Research Center, Louisville, KY 40292, USA
- Department of Bioinformatics and Biostatistics, University of Louisville School of Public Health and Information Sciences, Louisville, KY 40292, USA
- Biostatistics and Bioinformatics Facility, James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY 40292, USA
- The University of Louisville Superfund Research Center, Louisville, KY 40292, USA
| | - Kalina Andreeva
- Bioinformatics and Biomedical Computing Laboratory, Department of Computer Engineering and Computer Science, JB Speed School of Engineering, University of Louisville, Louisville, KY 40292, USA
| | - Eric C Rouchka
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Banrida Wahlang
- The University of Louisville Superfund Research Center, Louisville, KY 40292, USA
- Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Juliane I Beier
- Department of Medicine, Division of Gastroenterology, Hepatology & Nutrition, University of Pittsburgh, Louisville, KY 40292, USA
- Pittsburgh Liver Research Center (PLRC), Louisville, KY 40292, USA
- Department of Environmental and Occupational Health Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Matthew C Cave
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
- University of Louisville Hepatobiology and Toxicology Center, Louisville, KY 40292, USA
- University of Louisville Alcohol Research Center, Louisville, KY 40292, USA
- The University of Louisville Superfund Research Center, Louisville, KY 40292, USA
- Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40292, USA
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY 40292, USA
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20
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Wollen KL, Hagen L, Vågbø CB, Rabe R, Iveland TS, Aas PA, Sharma A, Sporsheim B, Erlandsen HO, Palibrk V, Bjørås M, Fonseca DM, Mosammaparast N, Slupphaug G. ALKBH3 partner ASCC3 mediates P-body formation and selective clearance of MMS-induced 1-methyladenosine and 3-methylcytosine from mRNA. J Transl Med 2021; 19:287. [PMID: 34217309 PMCID: PMC8254245 DOI: 10.1186/s12967-021-02948-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/17/2021] [Indexed: 02/07/2023] Open
Abstract
Background Reversible enzymatic methylation of mammalian mRNA is widespread and serves crucial regulatory functions, but little is known to what degree chemical alkylators mediate overlapping modifications and whether cells distinguish aberrant from canonical methylations. Methods Here we use quantitative mass spectrometry to determine the fate of chemically induced methylbases in the mRNA of human cells. Concomitant alteration in the mRNA binding proteome was analyzed by SILAC mass spectrometry. Results MMS induced prominent direct mRNA methylations that were chemically identical to endogenous methylbases. Transient loss of 40S ribosomal proteins from isolated mRNA suggests that aberrant methylbases mediate arrested translational initiation and potentially also no-go decay of the affected mRNA. Four proteins (ASCC3, YTHDC2, TRIM25 and GEMIN5) displayed increased mRNA binding after MMS treatment. ASCC3 is a binding partner of the DNA/RNA demethylase ALKBH3 and was recently shown to promote disassembly of collided ribosomes as part of the ribosome quality control (RQC) trigger complex. We find that ASCC3-deficient cells display delayed removal of MMS-induced 1-methyladenosine (m1A) and 3-methylcytosine (m3C) from mRNA and impaired formation of MMS-induced P-bodies. Conclusions Our findings conform to a model in which ASCC3-mediated disassembly of collided ribosomes allows demethylation of aberrant m1A and m3C by ALKBH3. Our findings constitute first evidence of selective sanitation of aberrant mRNA methylbases over their endogenous counterparts and warrant further studies on RNA-mediated effects of chemical alkylators commonly used in the clinic. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02948-6.
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Affiliation(s)
- Kristian Lied Wollen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway
| | - Lars Hagen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Trondheim, Norway
| | - Cathrine B Vågbø
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Trondheim, Norway
| | - Renana Rabe
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway
| | - Tobias S Iveland
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway
| | - Per Arne Aas
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway
| | - Animesh Sharma
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Trondheim, Norway
| | - Bjørnar Sporsheim
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway.,CMIC Cellular & Molecular Imaging Core Facility, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Trondheim, Norway
| | - Hilde O Erlandsen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Vuk Palibrk
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Davi M Fonseca
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Trondheim, Norway
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Geir Slupphaug
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway. .,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway. .,PROMEC Core Facility for Proteomics and Modomics, Norwegian University of Science and Technology, NTNU, and the Central Norway Regional Health Authority Norway, Trondheim, Norway.
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21
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Zhou D, Wang H, Bi F, Xing J, Gu Y, Wang C, Zhang M, Huang Y, Zeng J, Wu Q, Zhang Y. M6ADD: a comprehensive database of m 6A modifications in diseases. RNA Biol 2021; 18:2354-2362. [PMID: 33906563 PMCID: PMC8632072 DOI: 10.1080/15476286.2021.1913302] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
N6-methyladenosine (m6A) modification is an important regulatory factor affecting diseases, including multiple cancers and it is a developing direction for targeted disease therapy. Here, we present the M6ADD (m6A-diseases database) database, a public data resource containing manually curated data on potential m6A-disease associations for which some experimental evidence is available; the related high-throughput sequencing data are also provided and analysed by using different computational methods. To give researchers a tool to query the m6A modification data, the M6ADD was designed as a web-based comprehensive resource focusing on the collection, storage and online analysis of m6A modifications, aimed at exploring the associations between m6A modification and gene disorders and diseases. The M6ADD includes 222 experimentally confirmed m6A-disease associations, involving 59 diseases from a review of more than 2000 published papers. The M6ADD also includes 409,229 m6A-disease associations obtained by computational and statistical methods from 30 high-throughput sequencing datasets. In addition, we provide data on 5239 potential m6A regulatory proteins related to 24 cancers based on network analysis prediction methods. In addition, we have developed a tool to explore the function of m6A-modified genes through the protein-protein interaction networks. The M6ADD can be accessed at http://m6add.edbc.org/.
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Affiliation(s)
- Dianshuang Zhou
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Hongli Wang
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Fanqi Bi
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Jie Xing
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Yue Gu
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Cong Wang
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Menyan Zhang
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Yan Huang
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Jiaqi Zeng
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Qiong Wu
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Yan Zhang
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin, Heilongjiang, China.,State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
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22
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Zhang M, Song J, Yuan W, Zhang W, Sun Z. Roles of RNA Methylation on Tumor Immunity and Clinical Implications. Front Immunol 2021; 12:641507. [PMID: 33777035 PMCID: PMC7987906 DOI: 10.3389/fimmu.2021.641507] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/15/2021] [Indexed: 12/22/2022] Open
Abstract
RNA methylation is a kind of RNA modification that exists widely in eukaryotes and prokaryotes. RNA methylation occurs not only in mRNA but also in ncRNA. According to the different sites of methylation, RNA methylation includes m6A, m5C, m7G, and 2-O-methylation modifications. Modifications affect the splicing, nucleation, stability and immunogenicity of RNA. RNA methylation is involved in many physiological and pathological processes. In the immune system, especially for tumor immunity, RNA methylation affects the maturation and response function of immune cells. Through the influence of RNA immunogenicity and innate immune components, modifications regulate the innate immunity of the body. Some recent studies verified that RNA methylation can regulate tumor immunity, which also provides a new idea for the future of treating immunological diseases and tumor immunotherapy.
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Affiliation(s)
- Maorun Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Junmin Song
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Weitang Yuan
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenqiang Sun
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
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23
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Levi O, Arava YS. RNA modifications as a common denominator between tRNA and mRNA. Curr Genet 2021; 67:545-551. [PMID: 33683402 DOI: 10.1007/s00294-021-01168-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 12/27/2022]
Abstract
Recent studies underscore RNA modifications as a novel mechanism to coordinate expression and function of different genes. While modifications on the sugar or base moieties of tRNA are well known, their roles in mRNA regulation are only starting to emerge. Interestingly, some modifications are present in both tRNA and mRNA, and here we discuss the functional significance of these common features. We describe key modifications that are present in both RNA types, elaborate on proteins that interact with them, and indicate recent works that identify roles in communicating tRNA processes and mRNA regulation. We propose that as tools are developed, the shortlist of features that are common between types of RNA will greatly expand and proteins that interact with them will be identified. In conclusion, the presence of the same modification in both RNA types provides an intersect between tRNA processes and mRNA regulation and implies a novel mechanism for connecting diverse cellular processes.
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Affiliation(s)
- Ofri Levi
- Faculty of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Yoav S Arava
- Faculty of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel.
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